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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-08-15, 13:57 EDT based on data in: /work/gmgi/Fisheries/epiage/haddock/QC/raw_fastqc


        General Statistics

        Showing 279/279 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        Mae-263_S1_R1_001
        33.9%
        37%
        173.5M
        Mae-263_S1_R2_001
        33.0%
        37%
        173.5M
        Mae-265_S1_R2_001
        41.5%
        33%
        166.0M
        Mae-266_S2_R1_001
        30.8%
        36%
        182.2M
        Mae-266_S2_R2_001
        30.2%
        36%
        182.2M
        Mae-271_S2_R1_001
        37.9%
        33%
        130.9M
        Mae-271_S2_R2_001
        38.1%
        34%
        130.9M
        Mae-274_S3_R1_001
        41.9%
        35%
        142.2M
        Mae-274_S3_R2_001
        41.8%
        35%
        142.2M
        Mae-275_S3_R1_001
        31.7%
        38%
        100.1M
        Mae-275_S3_R2_001
        32.2%
        39%
        100.1M
        Mae-278_S4_R1_001
        37.8%
        35%
        142.0M
        Mae-278_S4_R2_001
        38.0%
        35%
        142.0M
        Mae-281_S5_R1_001
        41.9%
        37%
        182.7M
        Mae-281_S5_R2_001
        41.8%
        37%
        182.7M
        Mae-282_S4_R1_001
        40.1%
        33%
        190.8M
        Mae-282_S4_R2_001
        40.1%
        33%
        190.8M
        Mae-284_S5_R1_001
        42.6%
        33%
        138.3M
        Mae-284_S5_R2_001
        42.8%
        32%
        138.3M
        Mae-285_S6_R1_001
        43.5%
        37%
        148.6M
        Mae-285_S6_R2_001
        43.3%
        36%
        148.6M
        Mae-286_S6_R1_001
        31.9%
        36%
        123.5M
        Mae-286_S6_R2_001
        32.3%
        35%
        123.5M
        Mae-288_S7_R1_001
        35.0%
        38%
        123.5M
        Mae-288_S7_R2_001
        35.4%
        37%
        123.5M
        Mae-292_S8_R1_001
        28.8%
        36%
        107.2M
        Mae-292_S8_R2_001
        29.2%
        36%
        107.2M
        Mae-293_S7_R1_001
        38.9%
        35%
        161.7M
        Mae-293_S7_R2_001
        39.2%
        35%
        161.7M
        Mae-294_S8_R1_001
        45.9%
        33%
        190.0M
        Mae-294_S8_R2_001
        45.1%
        33%
        190.0M
        Mae-295_S9_R1_001
        38.5%
        36%
        117.6M
        Mae-295_S9_R2_001
        38.0%
        36%
        117.6M
        Mae-298_S10_R1_001
        37.3%
        37%
        155.6M
        Mae-298_S10_R2_001
        37.3%
        37%
        155.6M
        Mae-299_S9_R1_001
        29.8%
        36%
        87.6M
        Mae-299_S9_R2_001
        29.6%
        36%
        87.6M
        Mae-300_S10_R1_001
        33.1%
        36%
        136.9M
        Mae-300_S10_R2_001
        33.4%
        36%
        136.9M
        Mae-302_S11_R1_001
        45.5%
        35%
        117.0M
        Mae-302_S11_R2_001
        44.7%
        36%
        117.0M
        Mae-303_S11_R1_001
        32.6%
        36%
        124.3M
        Mae-303_S11_R2_001
        32.5%
        37%
        124.3M
        Mae-304_S12_R1_001
        34.4%
        36%
        161.9M
        Mae-304_S12_R2_001
        34.8%
        35%
        161.9M
        Mae-305_S12_R1_001
        44.8%
        36%
        145.1M
        Mae-305_S12_R2_001
        44.4%
        36%
        145.1M
        Mae-310_S13_R1_001
        37.2%
        36%
        179.9M
        Mae-310_S13_R2_001
        37.0%
        35%
        179.9M
        Mae-311_S14_R1_001
        38.8%
        35%
        191.3M
        Mae-311_S14_R2_001
        39.0%
        35%
        191.3M
        Mae-317_S15_R1_001
        41.5%
        34%
        147.9M
        Mae-317_S15_R2_001
        41.4%
        34%
        147.9M
        Mae-322_S16_R1_001
        33.6%
        36%
        189.9M
        Mae-322_S16_R2_001
        33.0%
        36%
        189.9M
        Mae-324_S13_R1_001
        36.6%
        34%
        160.6M
        Mae-324_S13_R2_001
        36.8%
        34%
        160.6M
        Mae-325_S14_R1_001
        31.7%
        35%
        131.1M
        Mae-325_S14_R2_001
        32.2%
        35%
        131.1M
        Mae-327_S17_R1_001
        39.3%
        34%
        99.8M
        Mae-327_S17_R2_001
        39.1%
        34%
        99.8M
        Mae-329_S18_R1_001
        39.1%
        35%
        142.3M
        Mae-329_S18_R2_001
        39.1%
        35%
        142.3M
        Mae-330_S19_R1_001
        38.1%
        36%
        219.2M
        Mae-330_S19_R2_001
        37.9%
        36%
        219.2M
        Mae-331_S15_R1_001
        47.6%
        31%
        149.2M
        Mae-331_S15_R2_001
        47.2%
        31%
        149.2M
        Mae-332_S16_R1_001
        32.0%
        36%
        173.1M
        Mae-332_S16_R2_001
        31.6%
        35%
        173.1M
        Mae-334_S17_R1_001
        33.5%
        35%
        111.9M
        Mae-334_S17_R2_001
        33.9%
        35%
        111.9M
        Mae-337_S18_R1_001
        41.0%
        33%
        157.7M
        Mae-337_S18_R2_001
        41.2%
        33%
        157.7M
        Mae-338_S20_R1_001
        37.5%
        35%
        188.8M
        Mae-338_S20_R2_001
        36.9%
        35%
        188.8M
        Mae-340_S19_R1_001
        40.8%
        32%
        187.8M
        Mae-340_S19_R2_001
        40.6%
        32%
        187.8M
        Mae-342_S21_R1_001
        42.9%
        34%
        230.9M
        Mae-342_S21_R2_001
        42.5%
        34%
        230.9M
        Mae-343_S22_R1_001
        32.9%
        36%
        222.4M
        Mae-343_S22_R2_001
        33.0%
        36%
        222.4M
        Mae-344_S23_R1_001
        38.6%
        36%
        217.2M
        Mae-344_S23_R2_001
        38.4%
        37%
        217.2M
        Mae-346_S20_R1_001
        40.1%
        35%
        163.3M
        Mae-346_S20_R2_001
        39.7%
        35%
        163.3M
        Mae-348_S21_R1_001
        35.7%
        35%
        186.8M
        Mae-348_S21_R2_001
        36.0%
        35%
        186.8M
        Mae-350_S24_R1_001
        43.0%
        38%
        167.2M
        Mae-350_S24_R2_001
        42.8%
        37%
        167.2M
        Mae-351_S22_R1_001
        33.5%
        32%
        138.2M
        Mae-351_S22_R2_001
        33.7%
        32%
        138.2M
        Mae-352_S25_R1_001
        32.5%
        37%
        130.6M
        Mae-352_S25_R2_001
        32.0%
        38%
        130.6M
        Mae-355_S23_R1_001
        36.4%
        33%
        184.8M
        Mae-355_S23_R2_001
        36.5%
        34%
        184.8M
        Mae-356_S26_R1_001
        33.5%
        37%
        143.4M
        Mae-356_S26_R2_001
        33.4%
        36%
        143.4M
        Mae-358_S24_R1_001
        39.5%
        33%
        260.0M
        Mae-358_S24_R2_001
        39.6%
        33%
        260.0M
        Mae-363_S25_R1_001
        40.3%
        31%
        132.0M
        Mae-363_S25_R2_001
        40.1%
        31%
        132.0M
        Mae-364_S26_R1_001
        41.7%
        32%
        144.4M
        Mae-364_S26_R2_001
        41.7%
        31%
        144.4M
        Mae-366_S27_R1_001
        42.4%
        32%
        130.9M
        Mae-366_S27_R2_001
        42.3%
        32%
        130.9M
        Mae-368_S27_R1_001
        33.5%
        36%
        134.5M
        Mae-368_S27_R2_001
        33.6%
        37%
        134.5M
        Mae-371_S28_R1_001
        34.1%
        36%
        115.5M
        Mae-371_S28_R2_001
        34.0%
        35%
        115.5M
        Mae-374_S28_R1_001
        39.2%
        33%
        122.0M
        Mae-374_S28_R2_001
        39.4%
        33%
        122.0M
        Mae-377_S29_R1_001
        33.3%
        33%
        141.4M
        Mae-377_S29_R2_001
        33.4%
        33%
        141.4M
        Mae-378_S29_R1_001
        37.7%
        35%
        103.3M
        Mae-378_S29_R2_001
        37.6%
        34%
        103.3M
        Mae-379_S71_R1_001
        33.4%
        34%
        185.9M
        Mae-379_S71_R2_001
        33.5%
        34%
        185.9M
        Mae-381_S30_R1_001
        39.9%
        33%
        164.8M
        Mae-381_S30_R2_001
        40.0%
        33%
        164.8M
        Mae-384_S72_R1_001
        33.4%
        33%
        125.1M
        Mae-384_S72_R2_001
        32.9%
        33%
        125.1M
        Mae-386_S31_R1_001
        33.3%
        33%
        132.4M
        Mae-386_S31_R2_001
        33.5%
        33%
        132.4M
        Mae-390_S32_R1_001
        42.5%
        36%
        220.8M
        Mae-390_S32_R2_001
        42.3%
        36%
        220.8M
        Mae-394_S32_R1_001
        37.1%
        33%
        186.7M
        Mae-394_S32_R2_001
        37.3%
        33%
        186.7M
        Mae-396_S33_R1_001
        32.1%
        36%
        113.8M
        Mae-396_S33_R2_001
        31.9%
        36%
        113.8M
        Mae-398_S33_R1_001
        30.6%
        33%
        105.0M
        Mae-398_S33_R2_001
        31.1%
        33%
        105.0M
        Mae-399_S34_R1_001
        30.0%
        36%
        128.5M
        Mae-399_S34_R2_001
        29.9%
        37%
        128.5M
        Mae-403_S35_R1_001
        32.9%
        36%
        118.1M
        Mae-403_S35_R2_001
        32.6%
        35%
        118.1M
        Mae-404_S34_R1_001
        38.4%
        31%
        169.2M
        Mae-404_S34_R2_001
        38.7%
        31%
        169.2M
        Mae-405_S36_R1_001
        29.5%
        36%
        93.2M
        Mae-405_S36_R2_001
        29.6%
        36%
        93.2M
        Mae-407_S35_R1_001
        44.7%
        32%
        226.5M
        Mae-407_S35_R2_001
        44.9%
        31%
        226.5M
        Mae-409_S36_R1_001
        29.1%
        33%
        102.5M
        Mae-409_S36_R2_001
        29.4%
        33%
        102.5M
        Mae-410_S37_R1_001
        38.0%
        35%
        127.4M
        Mae-410_S37_R2_001
        37.6%
        35%
        127.4M
        Mae-412_S37_R1_001
        34.5%
        32%
        147.8M
        Mae-412_S37_R2_001
        34.1%
        32%
        147.8M
        Mae-414_S38_R1_001
        33.2%
        37%
        108.5M
        Mae-414_S38_R2_001
        32.6%
        37%
        108.5M
        Mae-418_S38_R1_001
        31.0%
        34%
        179.6M
        Mae-418_S38_R2_001
        31.1%
        34%
        179.6M
        Mae-421_S39_R1_001
        34.1%
        37%
        129.5M
        Mae-421_S39_R2_001
        33.8%
        38%
        129.5M
        Mae-422_S40_R1_001
        30.0%
        37%
        98.4M
        Mae-422_S40_R2_001
        29.3%
        36%
        98.4M
        Mae-423_S39_R1_001
        35.7%
        32%
        176.4M
        Mae-423_S39_R2_001
        35.8%
        32%
        176.4M
        Mae-424_S41_R1_001
        30.6%
        38%
        106.1M
        Mae-424_S41_R2_001
        30.3%
        38%
        106.1M
        Mae-426_S40_R1_001
        34.5%
        32%
        151.3M
        Mae-426_S40_R2_001
        34.7%
        32%
        151.3M
        Mae-428_S42_R1_001
        36.4%
        36%
        116.1M
        Mae-428_S42_R2_001
        36.0%
        36%
        116.1M
        Mae-430_S51_R1_001
        35.3%
        32%
        140.9M
        Mae-430_S51_R2_001
        35.3%
        32%
        140.9M
        Mae-431_S41_R1_001
        35.5%
        33%
        149.0M
        Mae-431_S41_R2_001
        35.8%
        33%
        149.0M
        Mae-432_S43_R1_001
        31.5%
        36%
        124.8M
        Mae-432_S43_R2_001
        31.1%
        36%
        124.8M
        Mae-435_S42_R1_001
        30.4%
        33%
        174.6M
        Mae-435_S42_R2_001
        30.5%
        33%
        174.6M
        Mae-436_S44_R1_001
        27.9%
        36%
        130.0M
        Mae-436_S44_R2_001
        27.9%
        36%
        130.0M
        Mae-438_S43_R1_001
        31.2%
        33%
        181.7M
        Mae-438_S43_R2_001
        31.4%
        33%
        181.7M
        Mae-440_S45_R1_001
        34.1%
        37%
        117.9M
        Mae-440_S45_R2_001
        33.6%
        37%
        117.9M
        Mae-441_S46_R1_001
        31.8%
        37%
        118.1M
        Mae-441_S46_R2_001
        31.7%
        37%
        118.1M
        Mae-443_S44_R1_001
        33.0%
        33%
        131.0M
        Mae-443_S44_R2_001
        32.9%
        33%
        131.0M
        Mae-447_S45_R1_001
        40.5%
        31%
        109.0M
        Mae-447_S45_R2_001
        40.3%
        31%
        109.0M
        Mae-449_S48_R1_001
        33.9%
        36%
        189.0M
        Mae-449_S48_R2_001
        32.9%
        36%
        189.0M
        Mae-450_S46_R1_001
        38.4%
        30%
        147.1M
        Mae-450_S46_R2_001
        38.5%
        30%
        147.1M
        Mae-451_S47_R1_001
        37.9%
        33%
        162.6M
        Mae-451_S47_R2_001
        38.1%
        33%
        162.6M
        Mae-454_S49_R1_001
        29.4%
        36%
        91.3M
        Mae-454_S49_R2_001
        29.3%
        35%
        91.3M
        Mae-456_S48_R1_001
        35.4%
        33%
        90.7M
        Mae-456_S48_R2_001
        35.8%
        33%
        90.7M
        Mae-458_S49_R1_001
        36.9%
        32%
        114.8M
        Mae-458_S49_R2_001
        36.9%
        32%
        114.8M
        Mae-459_S50_R1_001
        34.0%
        33%
        182.9M
        Mae-459_S50_R2_001
        34.0%
        33%
        182.9M
        Mae-464_S50_R1_001
        45.3%
        34%
        100.8M
        Mae-464_S50_R2_001
        44.8%
        34%
        100.8M
        Mae-466_S52_R1_001
        36.9%
        30%
        119.4M
        Mae-466_S52_R2_001
        36.6%
        29%
        119.4M
        Mae-468_S51_R1_001
        38.7%
        36%
        163.2M
        Mae-468_S51_R2_001
        38.4%
        36%
        163.2M
        Mae-470_S52_R1_001
        39.0%
        35%
        116.2M
        Mae-470_S52_R2_001
        38.6%
        35%
        116.2M
        Mae-472_S53_R1_001
        34.7%
        29%
        100.7M
        Mae-472_S53_R2_001
        34.5%
        30%
        100.7M
        Mae-473_S54_R1_001
        29.0%
        33%
        88.2M
        Mae-473_S54_R2_001
        29.3%
        32%
        88.2M
        Mae-474_S57_R1_001
        35.9%
        38%
        179.5M
        Mae-474_S57_R2_001
        35.5%
        37%
        179.5M
        Mae-475_S53_R1_001
        32.6%
        35%
        131.0M
        Mae-475_S53_R2_001
        32.4%
        36%
        131.0M
        Mae-477_S54_R1_001
        36.3%
        37%
        160.3M
        Mae-477_S54_R2_001
        36.2%
        36%
        160.3M
        Mae-479_S55_R1_001
        42.3%
        32%
        141.5M
        Mae-479_S55_R2_001
        41.9%
        31%
        141.5M
        Mae-481_S55_R1_001
        35.9%
        36%
        191.9M
        Mae-481_S55_R2_001
        35.9%
        36%
        191.9M
        Mae-482_S56_R1_001
        35.2%
        30%
        112.4M
        Mae-482_S56_R2_001
        34.7%
        30%
        112.4M
        Mae-486_S57_R1_001
        46.8%
        30%
        156.6M
        Mae-486_S57_R2_001
        46.0%
        30%
        156.6M
        Mae-488_S56_R1_001
        31.3%
        35%
        142.2M
        Mae-488_S56_R2_001
        31.4%
        36%
        142.2M
        Mae-494_S58_R1_001
        29.1%
        31%
        78.3M
        Mae-494_S58_R2_001
        29.7%
        32%
        78.3M
        Mae-495_S47_R1_001
        48.0%
        34%
        141.4M
        Mae-495_S47_R2_001
        47.4%
        34%
        141.4M
        Mae-496_S58_R1_001
        42.6%
        32%
        139.7M
        Mae-496_S58_R2_001
        41.2%
        32%
        139.7M
        Mae-499_S59_R1_001
        41.4%
        36%
        188.1M
        Mae-499_S59_R2_001
        41.2%
        36%
        188.1M
        Mae-500_S59_R1_001
        36.0%
        31%
        101.1M
        Mae-500_S59_R2_001
        36.2%
        31%
        101.1M
        Mae-501_S60_R1_001
        39.3%
        36%
        212.7M
        Mae-501_S60_R2_001
        39.2%
        36%
        212.7M
        Mae-502_S61_R1_001
        38.2%
        37%
        168.2M
        Mae-502_S61_R2_001
        38.3%
        36%
        168.2M
        Mae-504_S60_R1_001
        41.0%
        30%
        146.3M
        Mae-504_S60_R2_001
        40.6%
        30%
        146.3M
        Mae-508_S61_R1_001
        32.1%
        33%
        244.2M
        Mae-508_S61_R2_001
        31.9%
        33%
        244.2M
        Mae-509_S62_R1_001
        36.5%
        36%
        203.4M
        Mae-509_S62_R2_001
        36.4%
        36%
        203.4M
        Mae-510_S62_R1_001
        44.0%
        30%
        169.8M
        Mae-510_S62_R2_001
        43.5%
        30%
        169.8M
        Mae-511_S63_R1_001
        38.4%
        31%
        190.2M
        Mae-511_S63_R2_001
        39.2%
        31%
        190.2M
        Mae-512_S63_R1_001
        36.6%
        36%
        202.4M
        Mae-512_S63_R2_001
        36.2%
        36%
        202.4M
        Mae-517_S64_R1_001
        39.3%
        30%
        120.7M
        Mae-517_S64_R2_001
        39.4%
        30%
        120.7M
        Mae-518_S65_R1_001
        29.0%
        36%
        122.1M
        Mae-518_S65_R2_001
        28.5%
        35%
        122.1M
        Mae-519_S64_R1_001
        36.9%
        36%
        144.9M
        Mae-519_S64_R2_001
        36.9%
        37%
        144.9M
        Mae-520_S65_R1_001
        37.6%
        36%
        151.9M
        Mae-520_S65_R2_001
        37.4%
        36%
        151.9M
        Mae-522_S66_R1_001
        33.2%
        35%
        265.2M
        Mae-522_S66_R2_001
        32.5%
        36%
        265.2M
        Mae-523_S67_R1_001
        41.7%
        35%
        214.9M
        Mae-523_S67_R2_001
        41.3%
        34%
        214.9M
        Mae-524_S66_R1_001
        40.6%
        35%
        163.4M
        Mae-524_S66_R2_001
        40.3%
        35%
        163.4M
        Mae-525_S67_R1_001
        33.3%
        36%
        200.9M
        Mae-525_S67_R2_001
        32.8%
        35%
        200.9M
        Mae-530_S68_R1_001
        31.6%
        35%
        124.1M
        Mae-530_S68_R2_001
        31.4%
        35%
        124.1M
        Mae-533_S68_R1_001
        37.8%
        37%
        228.7M
        Mae-533_S68_R2_001
        37.7%
        37%
        228.7M
        Mae-534_S69_R1_001
        32.7%
        35%
        161.7M
        Mae-534_S69_R2_001
        32.8%
        34%
        161.7M
        Mae-535_S69_R1_001
        36.9%
        37%
        213.8M
        Mae-535_S69_R2_001
        36.5%
        36%
        213.8M
        Mae-536_S70_R1_001
        32.5%
        34%
        162.1M
        Mae-536_S70_R2_001
        32.5%
        34%
        162.1M
        Mae-537_S70_R1_001
        32.8%
        35%
        247.2M
        Mae-537_S70_R2_001
        32.1%
        36%
        247.2M

        FastQC

        Version: 0.11.9

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (151bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 10/10 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        CACACACACACACACACACACACACACACACACACACACACACACACACA
        279
        181252041
        0.4266%
        ACACACACACACACACACACACACACACACACACACACACACACACACAC
        279
        140838754
        0.3314%
        GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
        277
        260595457
        0.6133%
        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        275
        115406467
        0.2716%
        TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
        240
        74896135
        0.1763%
        CCCAAAATAATTATAATACCACTCCCCACCATTTAAAAATAAAATTTATT
        9
        1405324
        0.0033%
        TATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
        4
        872878
        0.0021%
        CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
        4
        732863
        0.0017%
        ATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
        3
        527458
        0.0012%
        CCACACACACACACACACACACACACACACACACACACACACACACACAC
        1
        170098
        0.0004%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.11.9